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- PDB-1z91: x-ray crystal structure of apo-OhrRC15S in reduced form: MarR fam... -

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Basic information

Entry
Database: PDB / ID: 1z91
Titlex-ray crystal structure of apo-OhrRC15S in reduced form: MarR family protein
ComponentsOrganic hydroperoxide resistance transcriptional regulator
KeywordsDNA BINDING PROTEIN / OhrR / MarR family / Bacterial transcription factor
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to hydrogen peroxide / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
: / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Organic hydroperoxide resistance transcriptional regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHong, M. / Fuangthong, M. / Helmann, J.D. / Brennan, R.G.
CitationJournal: Mol.Cell / Year: 2005
Title: Structure of an OhrR-ohrA Operator Complex Reveals the DNA Binding Mechanism of the MarR Family.
Authors: Hong, M. / Fuangthong, M. / Helmann, J.D. / Brennan, R.G.
History
DepositionMar 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Organic hydroperoxide resistance transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)17,0101
Polymers17,0101
Non-polymers00
Water64936
1
A: Organic hydroperoxide resistance transcriptional regulator

A: Organic hydroperoxide resistance transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)34,0192
Polymers34,0192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4990 Å2
ΔGint-49 kcal/mol
Surface area14810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.355, 55.355, 77.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-178-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

#1: Protein Organic hydroperoxide resistance transcriptional regulator


Mass: 17009.727 Da / Num. of mol.: 1 / Mutation: C15S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ohrR / Plasmid: pET16x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: O34777
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.74 Å3/Da / Density % sol: 26.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30 to 33 % PEG 1450, 0.1 M ammonium acetate (or sodium acetate), and 0.1M sodium acetate, pH 4.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9794
SYNCHROTRONALS 8.2.120.9794, 0.9184, 0.9796
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJul 1, 2003
ADSC QUANTUM 2102CCDSep 30, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.91841
30.97961
ReflectionResolution: 2.5→45.175 Å / Num. all: 7251 / Num. obs: 4532 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.6 Å2
Reflection scaleGroup code: 1

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97947.59-8.25
13 wavelength20.91843.98-5.42
13 wavelength30.97964.4-15.52
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
19.84833.692.482SE601.06
229.82135.1537.742SE601.07
313.06130.230.717SE600.94
435.81510.3324.126SE601.11
518.89845.1977.194SE600.91
Phasing dm shellResolution: 3→500.01 Å / Delta phi final: 0.179 / FOM : 0.19 / Reflection: 3007

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→45 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 4233231.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.305 482 10.7 %RANDOM
Rwork0.223 ---
obs0.223 4484 99.6 %-
all-4491 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6333 Å2 / ksol: 0.359931 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.5 Å20 Å20 Å2
2---3.5 Å20 Å2
3---7.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 0 36 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.431.5
X-RAY DIFFRACTIONc_mcangle_it4.932
X-RAY DIFFRACTIONc_scbond_it5.42
X-RAY DIFFRACTIONc_scangle_it7.392.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 77 10.7 %
Rwork0.295 640 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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